Gracilicutes

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Gracilicutes
Escherichia coli cells magnified 25,000 times
Scientific classification Edit this classification
Domain:	Bacteria
(unranked):	Gracilicutes Gibbons and Murray 1978[1]
Superphyla/Phyla
Various definitions, see text

Gracilicutes (Latin: gracilis, slender, and cutis, skin, referring to the cell wall) is a clade in bacterial phylogeny.^[2]

Traditionally gram staining results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Monera (as the domains Bacteria and Archaea were known then) was divided into four phyla,^{[1] [3]}

• Gracilicutes (gram-negative, it is split in many groups, but some authors still use it in a narrower sense)
• Firmacutes [sic] (gram-positive, subsequently corrected to Firmicutes,^[4] today it excludes the Actinomycetota)
• Mollicutes (gram variable, later renamed Tenericutes and now Mycoplasmatota, e.g. Mycoplasma )
• Mendosicutes (uneven gram stain, "methanogenic bacteria" now known as methanogens and classed as Archaea)

This classification system was abandoned in favour of the three-domain system based on molecular phylogeny started by C. Woese.^{[5] [6]}

Using hand-drawn schematics rather than standard molecular phylogenetic analysis, Gracilicutes was revived in 2006 by Cavalier-Smith as an infrakindgom containing the phyla Spirochaetota, Sphingobacteria (FCB), Planctobacteria (PVC), and Proteobacteria.^[7] It is a gram-negative clade that branched off from other bacteria just before the evolutionary loss of the outer membrane or capsule, and just after the evolution of flagella.^[7] Most notably, this author assumed an unconventional tree of life placing Chloroflexota near the origin of life and Archaea as a close relative of Actinomycetota. This taxon is not generally accepted and the three-domain system is followed.^[8]

A taxon called Hydrobacteria was defined in 2009 from a molecular phylogenetic analysis of core genes. It is in contrast to the other major group of eubacteria called Terrabacteria .^[9] Some researchers have used the name Gracilicutes in place of Hydrobacteria , but this does not agree with the original description of Gracilicutes by Gibbons and Murray, noted above, which included cyanobacteria and did not follow the three-domain system. Also as noted above, the use of Gracilicutes by Cavalier-Smith can be rejected because it was a major alteration of an earlier taxonomic name, was not based on a statistical analysis, and did not follow the three-domain system. The most recent genomic analyses have supported the division of Bacteria into two major superphyla, corresponding to Terrabacteria and Hydrobacteria .^{[10] [11]}

The phylogenetic tree according to the phylogenetic analyzes of Battistuzzi and Hedges (2009) is the following and with a molecular clock calibration.^[9]

Recent phylogenetic analyzes have found that proteobacteria are a paraphyletic phylum that could encompass several recently discovered candidate phyla and other phyla such as Acidobacteriota, Chrysiogenota, Deferribacterota, and possibly Aquificota. This suggests that Gracilicutes or Hydrobacteria as a clade may comprise several candidates more closely related to Proteobacteria, Spirochaetes, PVC group, and FCB group than to bacteria from the clade Terrabacteria . Some of these phyla were classified as part of the proteobacteria. For example, Cavalier-Smith in his proposal of the 6 kingdoms included Acidobacteriota, Aquificota, Chrysiogenota, and Deferribacterota as part of the proteobacteria.^[7]

Phylogenetic analyzes have found roughly the following phylogeny between the major and some more closely related phyla.^{[12] [13] [14] [15]}